The submucosa is also identified in endoscopic ultrasound to identify the depth of tumours and to identify other abnormalities. An injection of dye, saline, or epinephrine into the submucosa is imperative in the safe removal of certain polyps.

Endoscopic mucosal resection involves removal of the mucosal layer, and in order to be done safely, a submucosal injection of dye is performed to ensure integrity at the beginning of the procedure.